tbuckley/cabot-search huggingface dataset:
HSR23-111: Real-World EGFR Testing in Patients With Surgically Resected Stage I-III Non–Small Cell Lung Cancer (NSCLC) in US Community Oncology Practices
Authors: Anne Shah, Jon Apple, Joanne Willey, Michael Ayars, Daniel Simmons, Dana Nickleach, Ganiat Mumuney, Manish Patel, Kristen Brunskill
Journal: Journal of the National Comprehensive Cancer Network (2023)

"HSR23-111: Real-World EGFR Testing in Patients With Surgically Resected Stage I-III Non–Small Cell Lung Cancer (NSCLC) in US Community Oncology Practices" published on 31 Mar 2023 by National Comprehensive Cancer Network.
Repetitive transcranial magnetic stimulation combined with cognitive training for cognitive function and activities of daily living in patients with post-stroke cognitive impairment: A systematic review and meta-analysis
Authors: Yong Gao, Yue Qiu, Qingyan Yang, Shaowen Tang, Jianqiu Gong, Hong Fan, Yuefeng Wu, Xiao Lu
Journal: Ageing Research Reviews (2023)
BPI23-016: Interventional Pain Management in Outpatient Setting for Cancer Patients: A Review of Literature
Authors: FNU Anamika, Akshit Chitkara, Anh-Tram Bui, Quang Nguyen, Arshia Adib, Pramil Cheriyath, Karamjeet Sandhu
Journal: Journal of the National Comprehensive Cancer Network (2023)
Neighborhood Incarceration Rates and Adverse Birth Outcomes in New York City, 2010-2014
Authors: Louisa W. Holaday, Destiny G. Tolliver, Tiana Moore, Keitra Thompson, Emily A. Wang
Journal: JAMA Network Open (2023)

Importance The US has high rates of adverse birth outcomes, with substantial racial disparities augmented by stress and neighborhood disadvantage. Black people are more likely to live in neighborhoods with high rates of incarceration, which is a source of both stress and neighborhood disadvantage and, thus, may contribute to adverse birth outcomes. Objective To determine whether neighborhoods with high incarceration rates also have higher rates of adverse birth outcomes compared with neighborhoods with lower rates. Design, Setting, and Participants This cross-sectional study used publicly available data from the New York City Department of Health (2010-2014). Censored Poisson regression, with the US Census tract as the unit of analysis, was used to examine the association of neighborhood incarceration rate and birth outcomes. Multivariable models included percentage of births aggregated to the Census tract by maternal factors (age, parity, singleton vs multiple birth, insurance, and race) and neighborhood factors (poverty, education, and violent crime). Analyses were performed between May 2021 and October 2022. Exposure Neighborhood incarceration rate, categorized into quintiles. Main Outcomes and Measures The primary outcome was the incidence rate ratio (IRR) of preterm birth and low birth weight. Secondary outcomes were IRRs of very preterm birth, extremely preterm birth, and very low birth weight. Hypotheses were formulated before data collection. Results Among 2061 Census tracts with 562 339 births, incarceration rates varied from 0 to 4545 people incarcerated per 100 000, and high-incarceration neighborhoods had more residents of Black race (54.00% vs 1.90%), living in poverty (32.30% vs 10.00%), and without a general educational development equivalent (28.00% vs 12.00%) compared with low-incarceration neighborhoods. In fully adjusted models, high-incarceration neighborhoods had a 13% higher IRR of preterm birth (IRR, 1.13; 95% CI, 1.08-1.18), 45% higher IRR of very preterm birth (IRR, 1.45; 95% CI, 1.24-1.71), 125% higher IRR of extremely preterm birth (IRR, 2.25; 95% CI, 1.59-3.18), 10% higher IRR of low birth weight (IRR, 1.10; 95% CI, 1.05-1.16), and 52% higher IRR of very low birth weight compared with low-incarceration neighborhoods (IRR, 1.52; 95% CI, 1.28-1.81). Conclusions and Relevance Neighborhood incarceration rate was positively associated with adverse birth outcomes, particularly those associated with infant mortality. Black people were significantly more likely to live in high-incarceration neighborhoods, suggesting that mass incarceration may contribute to racial disparities in birth outcomes.
QIM23-142: Evaluation of a Standardized Approach to Hypersensitivity/Infusion Reaction Management in a Large Ambulatory Oncology Center
Authors: Megan Corbett, Marylou Nesbitt, Bridget Scullion, Donna Marie Lynch, Mariana Castells, Yun Man, Terri Jabaley
Journal: Journal of the National Comprehensive Cancer Network (2023)

"QIM23-142: Evaluation of a Standardized Approach to Hypersensitivity/Infusion Reaction Management in a Large Ambulatory Oncology Center" published on 31 Mar 2023 by National Comprehensive Cancer Network.
Transformer guided progressive fusion network for 3D pancreas and pancreatic mass segmentation
Authors: Taiping Qu, Xiuli Li, Xiheng Wang, Wenyi Deng, Li Mao, Ming He, Xiao Li, Yun Wang, Zaiyi Liu, Longjiang Zhang, Zhengyu Jin, Huadan Xue, Yizhou Yu
Journal: Medical Image Analysis (2023)
CGE23-071: Real World Data on the Implementation of a Hereditary Hematological Myeloid Malignancy Workflow: Experience of a Single Academic Medical Center
Authors: Moon Ley Tung, Athena Puski, Jennifer L Stinson, Nicole Huser, Madeline VanDerGraaf
Journal: Journal of the National Comprehensive Cancer Network (2023)

"CGE23-071: Real World Data on the Implementation of a Hereditary Hematological Myeloid Malignancy Workflow: Experience of a Single Academic Medical Center" published on 31 Mar 2023 by National Comprehensive Cancer Network.
BPI23-012: Real-World Frequency of ECHO Monitoring and Incidence of Anti-HER2 Therapy Related Cardiac Events in HER2+ Breast Cancer Patients
Authors: Annette Hood, Blerina Mukallari, Jacqueline Majeski, Lajos Pusztai, Kerin Adelson, Kejal Amin
Journal: Journal of the National Comprehensive Cancer Network (2023)

"BPI23-012: Real-World Frequency of ECHO Monitoring and Incidence of Anti-HER2 Therapy Related Cardiac Events in HER2+ Breast Cancer Patients" published on 31 Mar 2023 by National Comprehensive Cancer Network.
ANXA1-derived peptide for targeting PD-L1 degradation inhibits tumor immune evasion in multiple cancers
Authors: Zheng-Zheng Yu, Yun-Ya Liu, Wei Zhu, Ding Xiao, Wei Huang, Shan-Shan Lu, Hong Yi, Ting Zeng, Xue-Ping Feng, Li Yuan, Jie-Ya Qiu, Di Wu, Qi Wen, Jian-Hua Zhou, Wei Zhuang, Zhi-Qiang Xiao
Journal: Journal for ImmunoTherapy of Cancer (2023)

Background Immune checkpoint inhibitors (ICIs) therapy targeting programmed cell death 1 (PD-1)/programmed cell death ligand 1 (PD-L1) shows promising clinical benefits. However, the relatively low response rate highlights the need to develop an alternative strategy to target PD-1/PD-L1 immune checkpoint. Our study focuses on the role and mechanism of annexin A1 (ANXA1)-derived peptide A11 degrading PD-L1 and the effect of A11 on tumor immune evasion in multiple cancers. Methods Binding of A11 to PD-L1 was identified by biotin pull-down coupled with mass spectrometry analysis. USP7 as PD-L1’s deubiquitinase was found by screening a human deubiquitinase cDNA library. The role and mechanism of A11 competing with USP7 to degrade PD-L1 were analyzed. The capability to enhance the T cell-mediated tumor cell killing activity and antitumor effect of A11 via suppressing tumor immune evasion were investigated. The synergistic antitumor effect of A11 and PD-L1 mAb (monoclonal antibody) via suppressing tumor immune evasion were also studied in mice. The expression and clinical significance of USP7 and PD-L1 in cancer tissues were evaluated by immunohistochemistry. Results A11 decreases PD-L1 protein stability and levels by ubiquitin proteasome pathway in breast cancer, lung cancer and melanoma cells. Mechanistically, A11 competes with PD-L1’s deubiquitinase USP7 for binding PD-L1, and then degrades PD-L1 by inhibiting USP7-mediated PD-L1 deubiquitination. Functionally, A11 promotes T cell ability of killing cancer cells in vitro, inhibits tumor immune evasion in mice via increasing the population and activation of CD8 + T cells in tumor microenvironment, and A11 and PD-1 mAb possess synergistic antitumor effect in mice. Moreover, expression levels of both USP7 and PD-L1 are significantly higher in breast cancer, non-small cell lung cancer and skin melanoma tissues than those in their corresponding normal tissues and are positively correlated in cancer tissues, and both proteins for predicting efficacy of PD-1 mAb immunotherapy and patient prognosis are superior to individual protein. Conclusion Our results reveal that A11 competes with USP7 to bind and degrade PD-L1 in cancer cells, A11 exhibits obvious antitumor effects and synergistic antitumor activity with PD-1 mAb via inhibiting tumor immune evasion and A11 can serve as an alternative strategy for ICIs therapy in multiple cancers.
Association Between Daily Alcohol Intake and Risk of All-Cause Mortality
Authors: Jinhui Zhao, Tim Stockwell, Tim Naimi, Sam Churchill, James Clay, Adam Sherk
Journal: JAMA Network Open (2023)

Importance A previous meta-analysis of the association between alcohol use and all-cause mortality found no statistically significant reductions in mortality risk at low levels of consumption compared with lifetime nondrinkers. However, the risk estimates may have been affected by the number and quality of studies then available, especially those for women and younger cohorts. Objective To investigate the association between alcohol use and all-cause mortality, and how sources of bias may change results. Data Sources A systematic search of PubMed and Web of Science was performed to identify studies published between January 1980 and July 2021. Study Selection Cohort studies were identified by systematic review to facilitate comparisons of studies with and without some degree of controls for biases affecting distinctions between abstainers and drinkers. The review identified 107 studies of alcohol use and all-cause mortality published from 1980 to July 2021. Data Extraction and Synthesis Mixed linear regression models were used to model relative risks, first pooled for all studies and then stratified by cohort median age (&amp;amp;lt;56 vs ≥56 years) and sex (male vs female). Data were analyzed from September 2021 to August 2022. Main Outcomes and Measures Relative risk estimates for the association between mean daily alcohol intake and all-cause mortality. Results There were 724 risk estimates of all-cause mortality due to alcohol intake from the 107 cohort studies (4 838 825 participants and 425 564 deaths available) for the analysis. In models adjusting for potential confounding effects of sampling variation, former drinker bias, and other prespecified study-level quality criteria, the meta-analysis of all 107 included studies found no significantly reduced risk of all-cause mortality among occasional (&amp;amp;gt;0 to &amp;amp;lt;1.3 g of ethanol per day; relative risk [RR], 0.96; 95% CI, 0.86-1.06; P = .41) or low-volume drinkers (1.3-24.0 g per day; RR, 0.93; P = .07) compared with lifetime nondrinkers. In the fully adjusted model, there was a nonsignificantly increased risk of all-cause mortality among drinkers who drank 25 to 44 g per day (RR, 1.05; P = .28) and significantly increased risk for drinkers who drank 45 to 64 and 65 or more grams per day (RR, 1.19 and 1.35; P &amp;amp;lt; .001). There were significantly larger risks of mortality among female drinkers compared with female lifetime nondrinkers (RR, 1.22; P = .03). Conclusions and Relevance In this updated systematic review and meta-analysis, daily low or moderate alcohol intake was not significantly associated with all-cause mortality risk, while increased risk was evident at higher consumption levels, starting at lower levels for women than men.
Macrophages facilitate tumor cell PD‐L1 expression via an IL‐1β‐centered loop to attenuate immune checkpoint blockade
Authors: Cheng Xu, Yu Xia, Bai‐Wei Zhang, Emmanuel Kwateng Drokow, Hua‐Yi Li, Sen Xu, Zhen Wang, Si‐Yuan Wang, Ping Jin, Tian Fang, Xiao‐Ming Xiong, Pu Huang, Ning Jin, Jia‐Hong Tan, Qing Zhong, Yu‐Xin Chen, Qi Zhang, Yong Fang, Fei Ye, Qing‐Lei Gao
Journal: MedComm (2023)

Abstract Tumor‐associated macrophages (TAMs) play critical roles in reprogramming other immune cells and orchestrating antitumor immunity. However, the interplay between TAMs and tumor cells responsible for enhancing immune evasion remains insufficiently understood. Here, we revealed that interleukin (IL)‐1β was among the most abundant cytokines within the in vitro tumor‐macrophage coculture system, and enhanced IL‐1β expression was associated with impaired cytotoxicity of CD8 + T cells in human ovarian cancer, indicating the possibility that IL‐1β mediated immunosuppression during tumor‐TAMs crosstalk. Mechanistically, we demonstrated that IL‐1β significantly boosted programmed death‐ligand 1 (PD‐L1) expression in tumor cells via the activation of the nuclear factor‐κb signaling cascade. Specifically, IL‐1β released from TAMs was triggered by lactate, the anaerobic metabolite of tumor cells, in an inflammasome activation‐dependent manner. IL‐1β sustained and intensified immunosuppression by promoting C‐C motif chemokine ligand 2 secretion in tumor cells to fuel TAMs recruitment. Importantly, IL‐1β neutralizing antibody significantly curbed tumor growth and displayed synergistic antitumor efficacies with anti‐PD‐L1 antibody in tumor‐bearing mouse models. Together, this study presents an IL‐1β‐centered immunosuppressive loop between TAMs and tumor cells, highlighting IL‐1β as a candidate therapeutic target to reverse immunosuppression and potentiate immune checkpoint blockade.
ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis
Authors: Jinlong Ru, Mohammadali Khan Mirzaei, Jinling Xue, Xue Peng, Li Deng
Journal: Gut Microbes (2023)

Bacteriophages play central roles in the maintenance and function of most ecosystems by regulating bacterial communities. Yet, our understanding of their diversity remains limited due to the lack of robust bioinformatics standards. Here we present ViroProfiler, an in-silico workflow for analyzing shotgun viral metagenomic data. ViroProfiler can be executed on a local Linux computer or cloud computing environments. It uses the containerization technique to ensure computational reproducibility and facilitate collaborative research. ViroProfiler is freely available at https://github.com/deng-lab/viroprofiler.
177Lu-DOTATATE Theranostics
Authors: Avery B. Peterson, Chang Wang, Ka Kit Wong, Kirk A. Frey, Otto Muzik, Matthew J. Schipper, Yuni K. Dewaraja
Journal: Clinical Nuclear Medicine (2023)

Purpose Pretreatment predictions of absorbed doses can be especially valuable for patient selection and dosimetry-guided individualization of radiopharmaceutical therapy. Our goal was to build regression models using pretherapy 68 Ga-DOTATATE PET uptake data and other baseline clinical factors/biomarkers to predict renal absorbed dose delivered by 177 Lu-DOTATATE peptide receptor radionuclide therapy ( 177 Lu-PRRT) for neuroendocrine tumors. We explore the combination of biomarkers and 68 Ga PET uptake metrics, hypothesizing that they will improve predictive power over univariable regression. Patients and Methods Pretherapy 68 Ga-DOTATATE PET/CTs were analyzed for 25 patients (50 kidneys) who also underwent quantitative 177 Lu SPECT/CT imaging at approximately 4, 24, 96, and 168 hours after cycle 1 of 177 Lu-PRRT. Kidneys were contoured on the CT of the PET/CT and SPECT/CT using validated deep learning–based tools. Dosimetry was performed by coupling the multi–time point SPECT/CT images with an in-house Monte Carlo code. Pretherapy renal PET SUV metrics, activity concentration per injected activity (Bq/mL/MBq), and other baseline clinical factors/biomarkers were investigated as predictors of the 177 Lu SPECT/CT-derived mean absorbed dose per injected activity to the kidneys using univariable and bivariable models. Leave-one-out cross-validation (LOOCV) was used to estimate model performance using root mean squared error and absolute percent error in predicted renal absorbed dose including mean absolute percent error (MAPE) and associated standard deviation (SD). Results The median therapy-delivered renal dose was 0.5 Gy/GBq (range, 0.2–1.0 Gy/GBq). In LOOCV of univariable models, PET uptake (Bq/mL/MBq) performs best with MAPE of 18.0% (SD = 13.3%), and estimated glomerular filtration rate (eGFR) gives an MAPE of 28.5% (SD = 19.2%). Bivariable regression with both PET uptake and eGFR gives LOOCV MAPE of 17.3% (SD = 11.8%), indicating minimal improvement over univariable models. Conclusions Pretherapy 68 Ga-DOTATATE PET renal uptake can be used to predict post- 177 Lu-PRRT SPECT-derived mean absorbed dose to the kidneys with accuracy within 18%, on average. Compared with PET uptake alone, including eGFR in the same model to account for patient-specific kinetics did not improve predictive power. Following further validation of these preliminary findings in an independent cohort, predictions using renal PET uptake can be used in the clinic for patient selection and individualization of treatment before initiating the first cycle of PRRT.
Objective measurement of retention of laparoscopic skills: a prospective cohort study
Authors: A. Masie Rahimi, Sem F. Hardon, Samuel R. Scholten, H. Jaap Bonjer, Freek Daams
Journal: International Journal of Surgery (2023)

There has been an overall growth of 462% in laparoscopic procedures performed by surgical residents between 2000 and 2018. Therefore, training courses in laparoscopic surgery are advocated in many postgraduate programs. While the immediate effect is determined in some cases, the retention of acquired skills is rarely investigated. The objective of this study was to objectively measure the retention of laparoscopic technical skills to offer a more personalized training program.First year general surgery residents performed two fundamental laparoscopic skills tasks (Post and Sleeve and the ZigZag loop) on the Lapron box trainer. Assessment was performed before, directly after, and 4 months after completing the basic laparoscopy course. Force, motion, and time were the measured variables.A total of 29 participants were included from 12 Dutch training hospitals and 174 trials were analyzed. The 4 months assessment of the Post and Sleeve showed a significant improvement in force ( P= 0.004), motion ( P ≤0.001), and time ( P ≤0.001) compared to the baseline assessment. The same was true for the ZigZag loop: force ( P ≤0.001), motion ( P= 0.005), and time ( P ≤0.001).Compared to the 4 months assessment, skill deterioration was present for the Post and Sleeve in the mean force ( P= 0.046), max impulse ( P= 0.12), and time ( P= 0.002). For the ZigZag loop, skill decay was observed for force ( P= 0.021), motion ( P= 0.015), and time ( P ≤0.001) parameters.Acquired laparoscopic technical skills decreased 4 months after the basic laparoscopy course. Compared to baseline performance, participants showed significant improvement, however deterioration was observed compared to postcourse measurements. To preserve acquired laparoscopic skills, it is recommended to incorporate maintenance training, preferably with objective parameters, in training curricula.
Tumor microenvironment signaling and therapeutics in cancer progression
Authors: Anshika Goenka, Fatima Khan, Bhupender Verma, Priyanka Sinha, Crismita C. Dmello, Manasi P. Jogalekar, Prakash Gangadaran, Byeong‐Cheol Ahn
Journal: Cancer Communications (2023)

Abstract Tumor development and metastasis are facilitated by the complex interactions between cancer cells and their microenvironment, which comprises stromal cells and extracellular matrix (ECM) components, among other factors. Stromal cells can adopt new phenotypes to promote tumor cell invasion. A deep understanding of the signaling pathways involved in cell‐to‐cell and cell‐to‐ECM interactions is needed to design effective intervention strategies that might interrupt these interactions. In this review, we describe the tumor microenvironment (TME) components and associated therapeutics. We discuss the clinical advances in the prevalent and newly discovered signaling pathways in the TME, the immune checkpoints and immunosuppressive chemokines, and currently used inhibitors targeting these pathways. These include both intrinsic and non‐autonomous tumor cell signaling pathways in the TME: protein kinase C (PKC) signaling, Notch, and transforming growth factor (TGF‐β) signaling, Endoplasmic Reticulum (ER) stress response, lactate signaling, Metabolic reprogramming, cyclic GMP–AMP synthase (cGAS)–stimulator of interferon genes (STING) and Siglec signaling pathways. We also discuss the recent advances in Programmed Cell Death Protein 1 (PD‐1), Cytotoxic T‐Lymphocyte Associated Protein 4 (CTLA4), T‐cell immunoglobulin mucin‐3 (TIM‐3) and Lymphocyte Activating Gene 3 (LAG3) immune checkpoint inhibitors along with the C‐C chemokine receptor 4 (CCR4)‐ C‐C class chemokines 22 (CCL22)/ and 17 (CCL17), C‐C chemokine receptor type 2 (CCR2)‐ chemokine (C‐C motif) ligand 2 (CCL2), C‐C chemokine receptor type 5 (CCR5)‐ chemokine (C‐C motif) ligand 3 (CCL3) chemokine signaling axis in the TME. In addition, this review provides a holistic understanding of the TME as we discuss the three‐dimensional and microfluidic models of the TME, which are believed to recapitulate the original characteristics of the patient tumor and hence may be used as a platform to study new mechanisms and screen for various anti‐cancer therapies. We further discuss the systemic influences of gut microbiota in TME reprogramming and treatment response. Overall, this review provides a comprehensive analysis of the diverse and most critical signaling pathways in the TME, highlighting the associated newest and critical preclinical and clinical studies along with their underlying biology. We highlight the importance of the most recent technologies of microfluidics and lab‐on‐chip models for TME research and also present an overview of extrinsic factors, such as the inhabitant human microbiome, which have the potential to modulate TME biology and drug responses.
Use of Active Surveillance vs Definitive Treatment Among Men With Low- and Favorable Intermediate–Risk Prostate Cancer in the US Between 2010 and 2018
Authors: Bashir Al Hussein Al Awamlh, Daniel A. Barocas, Alec Zhu, Jeffrey J. Tosoian, Lee Ponsky, Serban Negoita, Jonathan E. Shoag
Journal: JAMA Internal Medicine (2023)

This cross-sectional study of data from the Surveillance, Epidemiology and End Results database assesses temporal trends in the use of active surveillance and watchful waiting vs definitive treatment in men with low- and favorable intermediate–risk prostate cancer in the US between 2010 and 2018.
Association Between Use of Angiotensin Receptor Blockers and Incidence of Epilepsy in Patients With Hypertension—Reply
Authors: Corinna Doege, Mark Luedde, Karel Kostev
Journal: JAMA Neurology (2023)

In Reply We are grateful to Ryu and Kuo for their interesting and important comments on our publication, "Association Between Angiotensin Receptor Blocker Therapy and Incidence of Epilepsy in Patients with Hypertension.1" The authors addressed several points in their letter.
Comparative Effectiveness of Rituximab‐ Versus <scp>Cyclophosphamide‐Based</scp> Remission Induction Strategies in Antineutrophil Cytoplasmic Antibody–Associated Vasculitis for the Risk of Kidney Failure and Mortality
Authors: Zachary S. Wallace, Xiaoqing Fu, Claire Cook, Catherine Ahola, Zachary Williams, Brett Doliner, Jennifer S. Hanberg, John H. Stone, Yuqing Zhang, Hyon K. Choi
Journal: Arthritis & Rheumatology (2023)

To compare rituximab- versus cyclophosphamide-based remission induction strategies for the long-term risks of kidney failure and death in antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) in a real-world cohort.